AspGD Help: Protein Information Page
Contents
The AspGD Protein Information Page provides basic property, structure, and homology
information for all verified or predicted Aspergillus proteins.
The primary information is listed in the major column on the left of the page, and includes
links to interactive displays and other data resources.
The top of the protein page provides a site-wide quick search, links to the major AspGD informational resources,
and a bar with links to popular tools, such as a local BLAST search. Beneath this is a series of tabs linking to other
locus-specific information pages, including Locus Summary,
Locus History, Literature,
Gene Ontology, and
Phenotype. Several subtabs located just below the main Protein tab
provide access to more detailed information for conserved domains
and physicochemical properties.
-
- Standard Name and Systematic Name:
The protein names are based upon the gene names found on the Locus Summary page
(Aspergillus gene naming guidelines are described in the
Gene Nomenclature Guide).
Standard protein names for Aspergillus are non-italicized, and are derived from the corresponding
standard gene name by making the first character uppercase. For the systematic protein name, the
first character is uppercase and the remaining alphabetic characters are lowercase.
For example, the protein encoded by the gene veA (systematic name AN1052) has standard name VeA
and systematic name An1052.
- ORF classification:
- Verified: Direct experimental evidence exists for expression in Aspergillus.
- Uncharacterized: No direct experimental evidence, but likely to be biologically
significant based on comparative or statistical evidence.
See the AspGD
Sequence Documentation Page
for more details.
- Description:
A concise summary of the biological role and molecular function of the protein.
-
Summary of the predicted ORF translation, including:
- Length (a.a.): the predicted full length of the translated gene product.
- Molecular Weight (Da): calculated for the predicted full-length sequence.
- Isoelectric Point (pI): the pH at which the protein carries no net charge,
calculated using the BioPerl pICalculator module, which uses an algorithm described
here.
- A link to the Physicochemical Properties
page, which displays other properties and statistics calculated for the sequence.
- Predicted Sequence: the amino acid sequence itself, with a button to download the
sequence in FASTA format.
Provides:
- A link to the Domains/Motifs page, which lists
conserved features in the protein.
- A thumbnail image and link to the AspGD Proteome Browser,
which interactively displays conserved domains identified using the protein sequence to query the
InterPro database:
Provides links to several internal resources that can be used to identify homologs of the query protein, including:
- PDB homologs: Identifies homologs of known 3D structure.
- BLAST against other Aspergillus sequences: Runs BLAST locally using protein sequence as query
to identify Aspergillus homologs.
Provides links to various other databases containing the protein sequence.
References to publications accessed by AspGD curators in providing
functional descriptions of the protein and gene.
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